Scomber japonicus

chub mackerel

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


Resource Primary Assembly Alternate Assembly
GenBank fScoJap1: GCA_027409825.1 fScoJap1: GCA_027409835.1
ENA fScoJap1: GCA_027409825.1 fScoJap1: GCA_027409835.1
UCSC Genome Browser fScoJap1: GCA_027409825.1 fScoJap1: GCA_027409835.1

metadata.yaml (view) (edit on github)
species:
  short_name: fScoJap
  name: Scomber japonicus
  taxon_id: 13676
  common_name: chub mackerel
  order:
    name: Scombriformes
  family:
    name: Scombridae
  individuals:
    - short_name: fScoJap1
      provider: Chul Lee
  genome_size: 900000000
  genome_size_method:
  project: [ vgp ]
public domain NOAA (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fScoJap1 706.19 Gbp 784.66x 1.3 TiB
PacBio HiFi (.fq, Q≥20) fScoJap1 27.22 Gbp 30.24x 18.2 GiB
PacBio HiFi (.fq) fScoJap1 17.13 Gbp 19.03x 12.1 GiB
PacBio HiFi (.bam) fScoJap1 17.10 Gbp 19.00x 57.5 GiB
Arima fScoJap1 80.68 Gbp 89.64x 53.3 GiB
Illumina fScoJap1 38.95 Gbp 43.27x 18.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.90 Gbp.
Last upload on 15 January 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fScoJap1 PacBio HiFi (subreads) 706.19 Gbp 784.66x 1.3 TiB
PacBio HiFi (.fq, Q≥20) 27.22 Gbp 30.24x 18.2 GiB
PacBio HiFi (.fq) 17.13 Gbp 19.03x 12.1 GiB
PacBio HiFi (.bam) 17.10 Gbp 19.00x 57.5 GiB
Arima 80.68 Gbp 89.64x 53.3 GiB
Illumina 38.95 Gbp 43.27x 18.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.90 Gbp.
Last upload on 15 January 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 3 February 2022
fScoJap1.pri.cur.20220203.fasta.gz (227.8 MiB)

Quality: 1.7 errors/Mb (QV=57.75)

Contigs Scaffolds
NG LG Len LG Len
10 5 13.35 Mbp 2 40.75 Mbp
20 13 10.21 Mbp 4 39.92 Mbp
30 23 8.04 Mbp 6 36.93 Mbp
40 35 6.51 Mbp 9 36.02 Mbp
50 53 4.18 Mbp 11 34.19 Mbp
60 79 2.68 Mbp 14 32.59 Mbp
70 129 1.13 Mbp 17 31.46 Mbp
80 296 283.17 Kbp 20 29.06 Mbp
90 1199 37.87 Kbp 23 18.71 Mbp
100 0 0
0.920x 1932 0.83 Gbp 360 0.83 Gbp
NG based on genome size 0.90 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 3 February 2022
fScoJap1.alt.cur.20220203.fasta.gz (218.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 7.76 Mbp 9 7.76 Mbp
20 24 5.33 Mbp 24 5.33 Mbp
30 45 3.43 Mbp 45 3.43 Mbp
40 75 2.60 Mbp 75 2.60 Mbp
50 116 1.88 Mbp 116 1.88 Mbp
60 177 1.21 Mbp 177 1.21 Mbp
70 292 0.52 Mbp 292 0.52 Mbp
80 669 119.82 Kbp 669 119.82 Kbp
90 0 0
100 0 0
0.870x 2163 0.78 Gbp 2162 0.78 Gbp
NG based on genome size 0.90 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 June 2022
fScoJap1.MT.20220617.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/fScoJap1.yaml (view)
species: Scomber japonicus
specimen: fScoJap1
projects:
  - vgp
primary: s3://genomeark/species/Scomber_japonicus/fScoJap1/assembly_vgp_standard_2.0/fScoJap1.pri.asm.20211026.fasta.gz
haplotigs: s3://genomeark/species/Scomber_japonicus/fScoJap1/assembly_vgp_standard_2.0/fScoJap1.alt.asm.20211026.fasta.gz
hic_bam: s3://genomeark/species/Scomber_japonicus/fScoJap1/assembly_vgp_standard_2.0/evaluation/pretext/s2/fScoJap1_s2.bam
pretext: s3://genomeark/species/Scomber_japonicus/fScoJap1/assembly_vgp_standard_2.0/evaluation/pretext/s2/fScoJap1_s2.pretext
kmer_spectra_img: s3://genomeark/species/Scomber_japonicus/fScoJap1/assembly_vgp_standard_2.0/evaluation/merqury/p/fScoJap1_images/
pipeline:
  - hifiasm (0.15.4-r343)
  - purge_dups (1.2.5)
  - salsa (2.3)
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.